[English] 日本語
Yorodumi- PDB-3b32: Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b32 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-75 | ||||||
Components | Calmodulin | ||||||
Keywords | METAL BINDING PROTEIN / Calmodulin / EF hand motif / N-terminal domain / N-domain / Residues 1-75 / Methylation / Phosphorylation | ||||||
Function / homology | Function and homology information regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / presynaptic cytosol / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / spindle microtubule / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / Schaffer collateral - CA1 synapse / cellular response to type II interferon / G2/M transition of mitotic cell cycle / spindle pole / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / protein autophosphorylation / vesicle / transmembrane transporter binding / neuron projection / protein domain specific binding / positive regulation of apoptotic process / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Newman, R.A. / Shea, M.A. | ||||||
Citation | Journal: Methods Enzymol. / Year: 2009 Title: Thermodynamics and conformational change governing domain-domain interactions of calmodulin. Authors: O'Donnell, S.E. / Newman, R.A. / Witt, T.J. / Hultman, R. / Froehlig, J.R. / Christensen, A.P. / Shea, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3b32.cif.gz | 29.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3b32.ent.gz | 19.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b32_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3b32_full_validation.pdf.gz | 417.9 KB | Display | |
Data in XML | 3b32_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 3b32_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b32 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b32 | HTTPS FTP |
-Related structure data
Related structure data | 3ifkC 3clnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8323.156 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain Fragment, Residues 1-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): Lys-S / References: UniProt: P62161, UniProt: P0DP29*PLUS | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.62 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Na acetate, 0.01% Na azide, 21.25% PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2004 / Details: Osmic Blue Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→15.24 Å / Num. all: 11740 / Num. obs: 11740 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.3 / % possible all: 94.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CLN Resolution: 1.6→15.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.348 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.911 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
|